Grain filling rate is an important and complex agronomic trait that directly affects rice yield and quality. Huaidao 5， a superior rice japonica variety， derived from the 7208 ×Wuyujing 3 cross， shows a high grain filling rate， whereas its functional mechanism remains unclear. A transcriptome analysis in Huaidao 5 and Wuyujing 3 was performed by harvesting 14-days-after-fertilization grains. Real time fluorescent quantitative PCR was used to analyze the transcripts of few candidate genes， and Sanger sequencing was applied to identify their polymorphisms between Huaidao 5 and Wuyujing 3. 3230 up-regulated and 1171 down-regulated genes were detected between Huaidao 5 and Wuyujing 3. Gene ontology analysis indicated that these differentially-expressed genes were primarily involved in starch and sucrose biosynthesis， photosynthesis， carbon assimilation， and hormone biosynthesis and signaling transduction pathway. If compared to Wuyujing 3， more genes involved in starch and sucrose biosynthesis were up-regulated in Huaidao 5. Sixty-three hormone-related differentially expressed genes were detected， of which 38 genes were involved in the auxin pathway， suggesting that auxin plays an important role in the rice grain filling process. Several identified grain-filling-rate-related genes （GFR1， OsPFP1， OsPHO1；2， OsSWEET13， OsCIN2） were significantly up-regulated in Huaidao 5. Moreover， Sanger sequencing showed that GFR1^Huaidao5 might be an excellent haplotype to control the grain filling rate.